锡金海棠叶绿体基因组结构及密码子偏好性分析  

Analysis of Structure and Codon Usage Bias in the Chloroplast Genome of Malus sikkimensis

作　　者：陈玲慧 王慧[2] 刘岩 钱关泽[1] CHEN Linghui;WANG Hui;LIU Yan;QIAN Guanze(School of Life Science,Liaocheng University,Liaocheng 252059,China;Editorial Department,Journal of Liaocheng University,Liaocheng 252059,China)

机构地区：[1]聊城大学生命科学学院,山东聊城252059 [2]聊城大学学报编辑部,山东聊城252059

出　　处：《聊城大学学报（自然科学版）》2022年第6期96-103,共8页Journal of Liaocheng University:Natural Science Edition

基　　金：国家自然科学基金项目(31170178)资助。

摘　　要：为研究锡金海棠叶绿体基因组结构、明确其叶绿体基因组密码子使用模式,通过NOVOPlasty、geneious和codonW等软件,组装出锡金海棠叶绿体基因组,在注释后分析叶绿体基因组结构,并筛选出53条蛋白编码序列(CDS)用于密码子偏好性分析。结果表明,锡金海棠叶绿体基因组全长160088 bp,GC含量为36.6%;不同碱基位置GC含量分别为GC1(46.98%)>GC2(39.46%)>GC3(28.30%),表明其密码子末位碱基偏向以A/U结尾;中性图分析表明GC12与GC3未有明显相关性,即密码子第1、2位碱基与第3位碱基存在一定差异;根据ENC-plot和PR2-plot分析,影响密码子偏好性的主要因素是自然选择;最后确定UUG、CUU和AUU等14个密码子为锡金海棠叶绿体基因组的最优密码子。研究结果对今后研究锡金海棠亲缘关系、系统发育、物种鉴定提供了数据支持,对优化目标基因、种源的鉴定及异源表达基因的改造和系统发育分析提供了理论依据。In order to study the chloroplast genome structure of Malus sikkimensis and determine the use pattern of its chloroplast genome codon,the chloroplast genome of Malus sikkimensis was assembled using NOVOPlasty,Geneious and codonW software,and the chloroplast genome structure was analyzed after annotation.The 53 protein coding sequences(CDS)were screened for codon bias analysis.The results showed that the chloroplast genome of Malus sikkimensis was 160088bp with GC content of 36.6%.The GC contents of different base positions were GC1(46.98%)>GC2(39.46%)>GC3(28.30%),indicating that their codon terminal bases were biased to end with A/U.Neutrality plot analysis showed none significant correlation between GC12 and GC3,that is,there were some differences between the first and second bases of the codon and the third base.ENC-plot analysis and PR2-plot analysis show that codon preference is mainly affected by natural selection.Finally,14 codons,including UUG,CUU and AUU,were identified as the optimal codons for the chloroplast genome of Malus sikkimensis.The results of this study will provide data support for future studies on the kinship,phylogeny,and species identification of Malus sikkimensis,and provide a theoretical basis for optimizing target genes,seed identification,and heterologous expression gene modification.

关 键 词：锡金海棠 叶绿体基因组 密码子偏好性 

分 类 号：Q812[生物学—生物工程]